hitsz project for advancing protein sequences alignment using supervised contrastive learning

To install the model, please clone the repo first:

git clone https://github.com/jige114514/protein_alignment.git

Then in the folder, you should download the trained dedal model from the following link:

https://tfhub.dev/google/dedal/3

After that, there will be a folder called dedal_3 in this folder. Then you may install the necessary requirements by executing:

pip install -r requirements.txt

Then you can execute the code by running the following command, you can choose supervised or unsupervised dataset(supervised default):

python main.py --dataset supervised
python main.py --dataset unsupervised

In the process of executing, the program will output train loss and F1 scores of sequence pairs with distinct PID